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- PDB-1se9: Structure of At3g01050, a ubiquitin-fold protein from Arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 1se9
TitleStructure of At3g01050, a ubiquitin-fold protein from Arabidopsis thaliana
Componentsubiquitin family
KeywordsPLANT PROTEIN / ubiquitin-like / cell-free / wheat germ / Structural genomics / Protein structure Initiative / CESG / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


Membrane-anchored ubiquitin-fold protein / UBL3-like, ubiquitin domain / UBL3-like / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Membrane-anchored ubiquitin-fold protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics, cartesian molecular dynamics in explicit solvent
AuthorsVolkman, B.F. / Lytle, B.L. / Peterson, F.C. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Nat.Methods / Year: 2004
Title: Cell-free protein production and labeling protocol for NMR-based structural proteomics.
Authors: Vinarov, D.A. / Lytle, B.L. / Peterson, F.C. / Tyler, E.M. / Volkman, B.F. / Markley, J.L.
History
DepositionFeb 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ubiquitin family


Theoretical massNumber of molelcules
Total (without water)13,9701
Polymers13,9701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein ubiquitin family


Mass: 13970.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: At3g01050 / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: At3g01050 / Plasmid: PEU-AT3G01050 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9MAB9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY-aromatic
NMR detailsText: Chemical shift assignments were obtained from standard 3D triple-resonance experiments, using the automated method of Garant (Christian Bartels).

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Sample preparation

DetailsContents: 0.5 mM U-15N,13C At3g01050; 10mM phosphate buffer, 50mM KCl, 1mM DTT, pH 6.5
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM NaCl + 10 mM KPO4 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Peter Guentertrefinement
XwinNMR3.1Bruker Biospincollection
NMRPipe2.1Frank Delaglioprocessing
XPLOR-NIH2.0.6Marius Clorerefinement
XEASY1.3.1Christian Bartelsdata analysis
SPSCAN1.1.0Ralf Glaserdata analysis
RefinementMethod: torsion angle dynamics, cartesian molecular dynamics in explicit solvent
Software ordinal: 1
Details: CANDID automated refinement Cyana refinement Xplor water refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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